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Volumn 1, Issue 1, 2006, Pages

Reconstructing protein structure from solvent exposure using tabu search

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EID: 34248386800     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-1-20     Document Type: Article
Times cited : (11)

References (30)
  • 1
    • 0015222647 scopus 로고
    • The Interpretation of Protein Structures: Estimation of Static Accessibility
    • 10.1016/0022-2836(71)90324-X 5551392
    • Lee B Richards F The Interpretation of Protein Structures: Estimation of Static Accessibility J Mol Biol 1971 55 379-400 10.1016/ 0022-2836(71)90324-X 5551392
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.2
  • 2
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • 411235 272646 10.1073/pnas.75.1.303
    • Greer J Bush BL Macromolecular shape and surface maps by solvent exclusion Proc Natl Acad Sci USA 1978 75 303-7 411235 272646 10.1073/ pnas.75.1.303
    • (1978) Proc Natl Acad Sci USA , vol.75 , pp. 303-307
    • Greer, J.1    Bush, B.L.2
  • 3
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • 10.1126/science.6879170 6879170
    • Connolly ML Solvent-accessible surfaces of proteins and nucleic acids Science 1983 221 4612 709-13 10.1126/science.6879170 6879170
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.L.1
  • 4
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • 10.1016/S0969-2126(99)80097-5 10425675
    • Chakravarty S Varadarajan R Residue depth: A novel parameter for the analysis of protein structure and stability Structure 1999 7 7 723-32 10.1016/S0969-2126(99)80097-5 10425675
    • (1999) Structure , vol.7 , Issue.7 , pp. 723-732
    • Chakravarty, S.1    Varadarajan, R.2
  • 5
    • 1542606700 scopus 로고    scopus 로고
    • Atom depth in protein structure and function
    • 10.1016/j.tibs.2003.09.004 14607089
    • Pintar A Carugo O Pongor S Atom depth in protein structure and function Trends Biochem Sci 2003 28 11 593-7 10.1016/j.tibs.2003.09.004 14607089
    • (2003) Trends Biochem Sci , vol.28 , Issue.11 , pp. 593-597
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 6
    • 0037382258 scopus 로고    scopus 로고
    • Atom depth as a descriptor of the protein interior
    • 1302821 12668463
    • Pintar A Carugo O Pongor S Atom depth as a descriptor of the protein interior Biophys J 2003 84 4 2553-61 1302821 12668463
    • (2003) Biophys J , vol.84 , Issue.4 , pp. 2553-2561
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 7
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • 10.1002/prot.10069 11933061
    • Pollastri G Baldi P Fariselli P Casadio R Prediction of coordination number and relative solvent accessibility in proteins Proteins 2002 47 2 142-53 10.1002/prot.10069 11933061
    • (2002) Proteins , vol.47 , Issue.2 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 8
    • 10844226577 scopus 로고    scopus 로고
    • Predicting absolute contact numbers of native protein structure from amino acid sequence
    • 10.1002/prot.20300 15523668
    • Kinjo A Horimoto K Nishikawa K Predicting absolute contact numbers of native protein structure from amino acid sequence Proteins 2005 58 158-65 10.1002/prot.20300 15523668
    • (2005) Proteins , vol.58 , pp. 158-165
    • Kinjo, A.1    Horimoto, K.2    Nishikawa, K.3
  • 9
    • 14644400399 scopus 로고    scopus 로고
    • An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
    • 10.1002/prot.20379 15688434
    • Hamelryck T An amino acid has two sides: A new 2D measure provides a different view of solvent exposure Proteins 2005 59 38-48 10.1002/ prot.20379 15688434
    • (2005) Proteins , vol.59 , pp. 38-48
    • Hamelryck, T.1
  • 10
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • 10.1006/jmbi.1997.0959 9149153
    • Simons KT Kooperberg C Huang E Baker D Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J Mol Biol 1997 268 209-25 10.1006/jmbi.1997.0959 9149153
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 12
    • 19544367146 scopus 로고    scopus 로고
    • Recoverable one-dimensional encoding of three-dimensional protein structures
    • 10.1093/bioinformatics/bti330 15722374
    • Kinjo AR Nishikawa K Recoverable one-dimensional encoding of three-dimensional protein structures Bioinformatics 2005 21 10 2167-70 10.1093/bioinformatics/bti330 15722374
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2167-2170
    • Kinjo, A.R.1    Nishikawa, K.2
  • 13
    • 3142558004 scopus 로고    scopus 로고
    • Reconstruction of protein structures from a vectorial representation
    • Porto M Bastolla U Roman HE Vendruscolo M Reconstruction of protein structures from a vectorial representation Phys Rev Lett 2004 92 21
    • (2004) Phys Rev Lett , vol.92 , pp. 21
    • Porto, M.1    Bastolla, U.2    Roman, H.E.3    Vendruscolo, M.4
  • 14
    • 0346950252 scopus 로고    scopus 로고
    • Protein Conformation of a Lattice Model Using Tabu Search
    • 10.1023/A:1008228509535
    • Pardalos PM Liu X Xue GL Protein Conformation of a Lattice Model Using Tabu Search Journal of Global Optimization 1997 11 55-68 10.1023/ A:1008228509535
    • (1997) Journal of Global Optimization , vol.11 , pp. 55-68
    • Pardalos, P.M.1    Liu, X.2    Xue, G.L.3
  • 15
    • 0000918232 scopus 로고    scopus 로고
    • A parallel tabu search for conformational energy optimization of oligopeptides
    • 10.1002/(SICI)1096-987X(20000130)21:2<147::AID-JCC6>3.0.CO;2-6
    • Morales LB Garduño-Juárez R Aguilar-Alvarado JM Riveros-Castro FJ A parallel tabu search for conformational energy optimization of oligopeptides Journal of Computational Chemistry 2000 21 2 147-156 10.1002/ (SICI)1096-987X(20000130)21:2<147::AID-JCC6>3.0.CO;2-6
    • (2000) Journal of Computational Chemistry , vol.21 , Issue.2 , pp. 147-156
    • Morales, L.B.1    Garduño-Juárez, R.2    Aguilar-Alvarado, J.M.3    Riveros-Castro, F.J.4
  • 16
    • 27844612604 scopus 로고    scopus 로고
    • Lattice models of peptide aggregation: Evaluation of conformational search algorithms
    • 10.1002/jcc.20306 16170797
    • Oakley M Garibaldi J Hirst J Lattice models of peptide aggregation: Evaluation of conformational search algorithms J Comput Chem 2005 26 15 1638-46 10.1002/jcc.20306 16170797
    • (2005) J Comput Chem , vol.26 , Issue.15 , pp. 1638-1646
    • Oakley, M.1    Garibaldi, J.2    Hirst, J.3
  • 18
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • 10.1006/jmbi.1996.0175 8609636
    • Thomas PD Dill KA Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 1996 257 457-69 10.1006/ jmbi.1996.0175 8609636
    • (1996) J Mol Biol , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 19
    • 33644818869 scopus 로고    scopus 로고
    • Physical origins of protein superfamilies
    • 10.1016/j.jmb.2006.01.081 16483605
    • Zeldovich KB Berezovsky IN Shakhnovich EI Physical origins of protein superfamilies J Mol Biol 2006 357 4 1335-43 10.1016/j.jmb.2006.01.081 16483605
    • (2006) J Mol Biol , vol.357 , Issue.4 , pp. 1335-1343
    • Zeldovich, K.B.1    Berezovsky, I.N.2    Shakhnovich, E.I.3
  • 20
    • 33644760365 scopus 로고    scopus 로고
    • Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study
    • 1413881 16488978 10.1073/pnas.0508195103
    • Chikenji G Fujitsuka Y Takada S Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study Proc Natl Acad Sci USA 2006 103 3141-3146 1413881 16488978 10.1073/pnas.0508195103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 3141-3146
    • Chikenji, G.1    Fujitsuka, Y.2    Takada, S.3
  • 22
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • 10.1006/jmbi.1995.0311 7783205
    • Park B Levitt M The complexity and accuracy of discrete state models of protein structure J Mol Biol 1995 249 2 493-507 10.1006/jmbi.1995.0311 7783205
    • (1995) J Mol Biol , vol.249 , Issue.2 , pp. 493-507
    • Park, B.1    Levitt, M.2
  • 23
    • 0035964191 scopus 로고    scopus 로고
    • TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
    • 56926 11504922 10.1073/pnas.181328398
    • Kihara D Lu H Kolinski A Skolnick J TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints Proc Natl Acad Sci USA 2001 98 18 10125-30 56926 11504922 10.1073/pnas.181328398
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.18 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 24
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • 1303233 12885659
    • Zhang Y Kolinski A Skolnick J TOUCHSTONE II: A new approach to ab initio protein structure prediction Biophys J 2003 85 2 1145-64 1303233 12885659
    • (2003) Biophys J , vol.85 , Issue.2 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 25
    • 0000411214 scopus 로고
    • Tabu Search, PART I
    • Glover F Tabu Search, PART I ORSA J Comput 1989 1 190-206
    • (1989) ORSA J Comput , vol.1 , pp. 190-206
    • Glover, F.1
  • 26
    • 0001724713 scopus 로고
    • Tabu Search, PART II
    • Glover F Tabu Search, PART II ORSA J Comput 1990 2 4-32
    • (1990) ORSA J Comput , vol.2 , pp. 4-32
    • Glover, F.1
  • 27
    • 0025699780 scopus 로고
    • The Discrete P-Dispersion Problem
    • 10.1016/0377-2217(90)90297-O
    • Erkut E The Discrete P-Dispersion Problem European Journal of Operational Research 1990 46 48-60 10.1016/0377-2217(90)90297-O
    • (1990) European Journal of Operational Research , vol.46 , pp. 48-60
    • Erkut, E.1
  • 28
    • 0017636999 scopus 로고
    • Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins
    • 431666 271950 10.1073/pnas.74.12.5248
    • Rackovsky S Scheraga HA Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins Proc Natl Acad Sci USA 1977 74 12 5248-51 431666 271950 10.1073/pnas.74.12.5248
    • (1977) Proc Natl Acad Sci USA , vol.74 , Issue.12 , pp. 5248-5251
    • Rackovsky, S.1    Scheraga, H.A.2
  • 29
    • 27544446812 scopus 로고    scopus 로고
    • How do side chains orient globally in protein structures?
    • 10.1002/prot.20638 16152644
    • Yan A Jernigan RL How do side chains orient globally in protein structures? Proteins 2005 61 513-22 10.1002/prot.20638 16152644
    • (2005) Proteins , vol.61 , pp. 513-522
    • Yan, A.1    Jernigan, R.L.2
  • 30
    • 35949020425 scopus 로고
    • Replica Monte Carlo simulation of spin glasses
    • 10.1103/PhysRevLett.57.2607 10033814
    • Swendsen RH Wang JS Replica Monte Carlo simulation of spin glasses PHYSICAL REVIEW LETTERS 1986 57 21 2607-2609 10.1103/PhysRevLett.57.2607 10033814
    • (1986) Physical Review Letters , vol.57 , Issue.21 , pp. 2607-2609
    • Swendsen, R.H.1    Wang, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.